title: Multiscale geometric modeling of macromolecules II: Lagrangian representation.
abstract: Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR, and cryo-electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation, and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions.
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Feng
authors.forename: Kelin
authors.initials: K
authors.lastname: Xia
authors.forename: Zhan
authors.initials: Z
authors.lastname: Chen
authors.forename: Yiying
authors.initials: Y
authors.lastname: Tong
authors.forename: Guo-Wei
authors.initials: GW
authors.lastname: Wei
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D011506:Proteins
keywords: curvature; electrostatics; energy functional; meshing; multiresolution surface; variational multiscale modeling